Prepare release 1.1

ViennaRNA · Feb 6, 2018 · 19b06dd · 19b06dd
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diff --git a/doc/apidoc/forgi.graph.rst b/doc/apidoc/forgi.graph.rst
@@ -1,13 +1,18 @@
-The package forgi\.graph
-========================
+forgi\.graph package
+====================
 
-This only contains the module forgi.graph.bulge_graph.
-It contains the BulgeGraph datastructure for storing an RNA.
+Submodules
+----------
 
-forgi\.graph\.bulge_graph module
---------------------------------
+.. toctree::
 
-.. automodule:: forgi.graph.bulge_graph
+   forgi.graph.bulge_graph
+   forgi.graph.residue
+
+Module contents
+---------------
+
+.. automodule:: forgi.graph
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/doc/changelog.rst b/doc/changelog.rst
@@ -1,6 +1,22 @@
 Changelog
 =========
 
+Changes in Version 1.1
+----------------------
+
+*  We now support **DSSR** as an alternative to **MC-Annotate**.
+   See the :ref:`installation` for more information
+*  RESID for pdb-derived residue ids in now moved into a seperate module.
+*  `describe_cg.py` now adds the number of the multiloop in the sequence to the generated csv.
+*  **Bugfixes**:
+
+   *  python3 compatibility of `visualize_cg.py`
+   *  windows-compatibility of `visualize_cg.py`
+   *  fix count of multiloop-types in `describe_cg.py`
+   *  persist cofold-breakpoints in cg-files, even if no sequence was given.
+   *  fix bugs in parsing of MC-Annotate output. Forgi should now be able to load most pdb-files.
+   *  properly propagate the `--keep-length-one-stems` option.
+
 Changes in Version 1.0
 ----------------------
 

diff --git a/doc/conf.py b/doc/conf.py
@@ -50,9 +50,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0'
+version = '1.1'
 # The full version, including alpha/beta/rc tags.
-release = '1.0'
+release = '1.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/download.rst b/doc/download.rst
@@ -58,8 +58,14 @@ MC-Annotate is available at http://major.iric.ca/MajorLabEn/MC-Tools.html
 DSSR is available at http://home.x3dna.org/
 
 You can create a configuration file to decide which of the two programs you want to use.
-If no configuration file exists, you will be prompted to choose the program the first time you
-convert a PDB file. Your choice will be recorded in a newly generated configuration file.
+If no configuration file exists, MC-Annotate will be used.
 
 We use the appdirs package to define the system specific location of the
 configuration file. Under Linux it would default to ~/.config/forgi.
+Under Linux, you can create the configuration file like this::
+
+  echo '{"PDB_ANNOTATION_TOOL": "MC-Annotate"}' >  ~/.config/forgi/config.json
+
+or::
+
+  echo '{"PDB_ANNOTATION_TOOL": "DSSR"}' >  ~/.config/forgi/config.json
diff --git a/doc/index.rst b/doc/index.rst
@@ -3,7 +3,7 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-forgi 1.0
+forgi 1.1
 =================================
 
 forgi is a python library for manipulating RNA secondary structure. Some examples of its usage can be found in the two tutorials below. Please note that forgi is under development and can be a little unstable. Names and interfaces might change. If you are using this library and something changes to break your work, please do let me know and I'll try and sort it out.

diff --git a/doc/threedee_tutorial.rst b/doc/threedee_tutorial.rst
@@ -12,9 +12,9 @@ well as creating a coarse grain representation of 3D RNA structures.
 Requirements
 ~~~~~~~~~~~~
 
-MC_Annotate_ is required for annotating the nucleotide interactions.
+MC_Annotate or DSSR is required for annotating the nucleotide interactions.
+See :ref:`installation`
 
-.. _MC_Annotate: http://www.major.iric.ca/MajorLabEn/MC-Tools.html
 
 Extracting 2D structure from a 3D structure
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/forgi/__init__.py b/forgi/__init__.py
@@ -1,7 +1,7 @@
 __author__ = "Peter Kerpedjiev, Bernhard Thiel"
 __copyright__ = "Copyright 2012 - 2016"
 __license__ = "GNU Affero GPL v 3.0"
-__version__ = "1.0"
+__version__ = "1.1"
 __maintainer__ = "Bernhard Thiel"
 __email__ = "[email protected]"
 

diff --git a/forgi/graph/bulge_graph.py b/forgi/graph/bulge_graph.py
@@ -3319,14 +3319,15 @@ def get_angle_type(self, bulge, allow_broken = False):
         spanning tree.
 
         :param allow_broken: How to treat broken multiloop segments.
-                             * False (default): Return None
-                             * The string "bo" or "build_order": Return the
-                               angle type according to the build-order
-                               (i.e. from the first built stem to the last-built stem)
-                             * True: Return the angle_type from the stem with
-                               lower nt number to the stem with higher nt number.
-                               In forgi 2.0 this will be removed and the behavior of "bo"
-                               will be used instead.
+        
+                             *  False (default): Return None
+                             *  The string "bo" or "build_order": Return the
+                                angle type according to the build-order
+                                (i.e. from the first built stem to the last-built stem)
+                             *  True: Return the angle_type from the stem with
+                                lower nt number to the stem with higher nt number.
+                                In forgi 2.0 this will be removed and the behavior of "bo"
+                                will be used instead.
         """
         if self.ang_types is None:
             self.set_angle_types()

diff --git a/forgi/utilities/commandline_utils.py b/forgi/utilities/commandline_utils.py
@@ -140,15 +140,16 @@ def load_rna(filename, rna_type="any", allow_many=True, pdb_chain=None,
              dissolve_length_one_stems = True):
     """
     :param rna_type: One of "any", "cg" and "3d" and "pdb"
-                     "any": Return either BulgeGraph or CoarseGrainRNA objekte,
+
+                     *  "any": Return either BulgeGraph or CoarseGrainRNA objekte,
                             depending on the input format
-                     "cg":  Always convert to CoarseGrainRNA objects,
+                     *  "cg":  Always convert to CoarseGrainRNA objects,
                             even if they have no 3D information
-                     "only_cg": Only accept cg-files.
-                     "3d":  Return CoarseGrainRNA objects,
+                     *  "only_cg": Only accept cg-files.
+                     *  "3d":  Return CoarseGrainRNA objects,
                             if the file contains 3D information,
                             raise an error otherwise
-                     "pdb": only accept pdb files
+                     *  "pdb": only accept pdb files
     :param allow_many: If True, return a list. If False raise an error, if more than one RNA is present.
     :param pdb_chain: Extract the given chain from the file.
                       Only applicable if filename corresponds to a pdb file

diff --git a/setup.py b/setup.py
@@ -34,7 +34,7 @@ def run(self):
 setup(
       cmdclass={'build_py': build_py},
       name='forgi',
-      version='1.0',
+      version='1.1',
       description='RNA Graph Library',
       author='Peter Kerpedjiev, Bernhard Thiel',
       author_email='[email protected], [email protected]',